Remove abandoned filter project and unneeded build dependency (#7950)

build.gradle

@@ -363,9 +363,6 @@ dependencies {
     // Required for COSMIC Funcotator data source:
     implementation 'org.xerial:sqlite-jdbc:3.36.0.3'
 
-    // Required for SV Discovery machine learning
-    implementation group: 'biz.k11i', name: 'xgboost-predictor', version: '0.3.0'
-
     // natural sort
     implementation('net.grey-panther:natural-comparator:1.1')
     implementation('com.fasterxml.jackson.module:jackson-module-scala_' + scalaVersion + ':2.9.8')

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/StructuralVariationDiscoveryArgumentCollection.java

@@ -118,12 +118,7 @@ public static class FindBreakpointEvidenceSparkArgumentCollection implements Ser
                 fullName = "sv-evidence-filter-threshold-probability")
         public double svEvidenceFilterThresholdProbability = 0.92;
 
-        @Argument(doc = "Filter method for selecting evidence to group into Assembly Intervals",
-                fullName = "sv-evidence-filter-type")
-        public SvEvidenceFilterType svEvidenceFilterType = SvEvidenceFilterType.DENSITY;
-
         // ---------- options -----------
-
         @Argument(doc = "Write GFA representation of assemblies in fastq-dir.", fullName = "write-gfas")
         public boolean writeGFAs = false;
 
@@ -267,8 +262,6 @@ public void validate() {
         }
     }
 
-    public enum SvEvidenceFilterType {DENSITY, XGBOOST}
-
     public static class DiscoverVariantsFromContigAlignmentsArgumentCollection implements Serializable {
         private static final long serialVersionUID = 1L;
 

src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/FindBreakpointEvidenceSpark.java

@@ -1115,17 +1115,10 @@ private static Iterator<BreakpointEvidence> getFilter(
             final StructuralVariationDiscoveryArgumentCollection.FindBreakpointEvidenceSparkArgumentCollection params,
             final PartitionCrossingChecker partitionCrossingChecker
     ) {
-        switch(params.svEvidenceFilterType) {
-            case DENSITY:
-                return new BreakpointDensityFilter(
-                        evidenceItr, readMetadata, params.minEvidenceWeightPerCoverage,
-                        params.minCoherentEvidenceWeightPerCoverage, partitionCrossingChecker, params.minEvidenceMapQ
-                );
-            case XGBOOST:
-                return new XGBoostEvidenceFilter(evidenceItr, readMetadata, params, partitionCrossingChecker);
-            default:
-                throw new IllegalStateException("Unknown svEvidenceFilterType: " + params.svEvidenceFilterType);
-        }
+        return new BreakpointDensityFilter(
+            evidenceItr, readMetadata, params.minEvidenceWeightPerCoverage,
+            params.minCoherentEvidenceWeightPerCoverage, partitionCrossingChecker, params.minEvidenceMapQ
+        );
     }
 
     private static void writeTargetLinks(final Broadcast<ReadMetadata> broadcastMetadata,